rs7937421

Variant names:

• chr11-31274126-T-C
• rs7937421
• NM_001387274.1:c.961-8526A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001387274.1(DCDC1):​c.961-8526A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,114 control chromosomes in the GnomAD database, including 5,383 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.26 (5383 hom., cov: 32)
• Consequence: DCDC1 NM_001387274.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.977
• Publications: 2 publications found

Genes affected

DCDC1 (HGNC:20625): (doublecortin domain containing 1) This gene encodes a member of the doublecortin family. The protein encoded by this gene is a hydrophilic, intracellular protein. It contains a single doublecortin domain and is unable to bind microtubules and to regulate microtubule polymerization. This gene is mainly expressed in adult testis. It does not have a mouse homolog. [provided by RefSeq, Sep 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCDC1	NM_001387274.1	c.961-8526A>G		intron_variant	Intron 7 of 38	ENST00000684477.1	NP_001374203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCDC1	ENST00000684477.1	c.961-8526A>G		intron_variant	Intron 7 of 38		NM_001387274.1	ENSP00000507427.1
DCDC1	ENST00000452803.1	c.961-8526A>G		intron_variant	Intron 7 of 8	1		ENSP00000389792.1
DCDC1	ENST00000597505.5	c.961-8526A>G		intron_variant	Intron 5 of 35	5		ENSP00000472625.1
DCDC1	ENST00000342355.8	n.755-8526A>G		intron_variant	Intron 6 of 21	2		ENSP00000343496.4

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39831 AN: 151996 Hom.: 5373 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.265

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.262 AC: 39867 AN: 152114 Hom.: 5383 Cov.: 32 AF XY: 0.257 AC XY: 19118 AN XY: 74386

African (AFR) AF: 0.318 AC: 13202 AN: 41480

American (AMR) AF: 0.260 AC: 3975 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1537 AN: 5164

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4826

European-Finnish (FIN) AF: 0.135 AC: 1429 AN: 10596

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16621 AN: 67974

Other (OTH) AF: 0.275 AC: 580 AN: 2110

Alfa AF: 0.255 Hom.: 615

Bravo AF: 0.272

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.84
PhyloP100		0.98
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7937421; hg19: chr11-31295673; COSMIC: COSV60858870;